Pesticides are reported to be teratogenic for non-target species. Our studies have unraveled the teratogenicity of 50 % Chlorpyrifos & 5 % Cypermethrin combination (Ci) in developing chick embryos. A sub-lethal dose of this combination when administered to chick embryos, caused several developmental anomalies, with defects in eye development being frequent. Eye development begins at an early embryonic stage, with Sonic hedgehog (Shh) serving as a crucial signaling molecule. Shh plays a pivotal role in the early development of multiple organs, including the eye, by interacting with Pax6 and other regulatory molecules to guide the proper patterning of the eye. Thus, we hypothesized that Ci administration may lead to alteration in Shh expression which subsequently hampers downstream signaling molecules potentially contributing to congenital eye defects. Morphological, anatomical, histological, transcriptional and protein level analyses at various stages (Days 1,2,4 and 10) were carried out to evaluate the hypothesis. The results revealed a remarkable alteration of key regulators in treated embryos compared to control, providing insights into plausible causative mechanisms underlying Ci-induced congenital eye defects.